BioC API for PMC Open Access

Overview

The BioC API provides full-text articles from PubMed Central (PMC) in the BioC format — a simplified XML/JSON structure designed specifically for biomedical text mining. Unlike the standard PMC OAI service (which returns JATS XML), BioC pre-segments text into passages with offset annotations, making it ideal for NLP pipelines, named entity recognition, relation extraction, and other text mining tasks. Free, no authentication required.

API Endpoints

Base URL

https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/{PMCID}/unicode

Retrieve by PMC ID

# JSON format (recommended for programmatic use)
curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC6267067/unicode"

# XML format
curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC6267067/unicode"

# ASCII encoding (strips non-ASCII characters)
curl "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC6267067/ascii"

Retrieve by PubMed ID

# Convert PMID to PMCID first, then query
curl "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=29346600&format=json"
# Returns: {"records": [{"pmid": "29346600", "pmcid": "PMC6267067", ...}]}

BioC JSON Structure

{
  "source": "PMC",
  "date": "2024-01-15",
  "key": "collection.key",
  "documents": [
    {
      "id": "PMC6267067",
      "passages": [
        {
          "infons": {
            "section_type": "TITLE",
            "type": "title"
          },
          "offset": 0,
          "text": "Article Title Here"
        },
        {
          "infons": {
            "section_type": "ABSTRACT",
            "type": "abstract"
          },
          "offset": 25,
          "text": "Background: This study investigates..."
        },
        {
          "infons": {
            "section_type": "INTRO",
            "type": "paragraph"
          },
          "offset": 350,
          "text": "The introduction text..."
        }
      ]
    }
  ]
}